Topological Patterns in Gel Electrophoresis of DNA Knots

Agarose gels are broadly employed across the biophysical community. Beyond being an ideal environment for the growth of bacterial colonies, agarose gels are also commonly used to identify and classify biomolecules based on their physical properties. Electrophoresis of charged biopolymers through agarose gels is in fact an important tool to discriminate their weight, length or topology. Although the patterns of bands and spots emerging from 1D and 2D gel electrophoresis are empirically widely accepted, at present there is no theoretical model that can explain all the observed "topological patterns" from first principles. Particularly complicated and puzzling patterns have been observed for viral DNA, which is known to be heavily knotted.

In order to shed some light into this problem, I will describe a crude model for agarose gels which improves previous attempts to capture its porous structure and then show that accounting for the gel's microscopic disorder (under the form of "dangling ends") crucially allows one to capture some of the unexplained topological patterns observed for gel electrophoresis of circular and knotted DNA.